← BioTransfer GEO Dataset Finder
GEO series

Stepwise de novo establishment of inactive X chromosome architecture in early development

GSE206011 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 262 samples Submitted 2024/09/10 Platform GPL24247Platform GPL21273
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 262 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
262 samples: 85 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Stepwise de novo establishment of inactive X chromosome architecture in early developmentNature genetics · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Stepwise de novo establishment of inactive X chromosome architecture in early development
Du Z, Hu L, Zou Z et al. · Nature genetics 2024 · PMID 39256583 · doi:10.1038/s41588-024-01897-2
This dataset
Open GSE206011 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE206011_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA848784 and SRA study SRP379885. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39256583) ↗
Study design
85 conditions, mostly in duplicate
E7.5 extraembryonic ectoderm, EedmNull, femal… ×13 E7.5 extraembryonic ectoderm, EedmNull, femal… ×13 Hi-C XEN cells, Rad21-degron, dTAG treated, c… ×7 Hi-C XEN cells, WT, ×6 Hi-C XEN cells, Rad21-degron, DMSO treated, c… ×4 RNA-seq XEN cells, XistpA, ×4 DNA Morula, control, male, ×4 DNA Morula, Xp XRRa KO, female, ×4 +111 more

Supports a case/control comparison: 24 samples read as cases, 32 as controls.

How we read this: 85 replicated groups read from 262 sample titles; they account for 228 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 222 more — browse all 262 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.